AMBER Archive (2007)

Subject: Re: AMBER: Atoms closer to 2 angstroms to each other

From: David A. Case (case_at_scripps.edu)
Date: Mon May 07 2007 - 09:55:30 CDT

On Mon, May 07, 2007, Christopher Gaughan wrote:
>
> I would like to put a TER card after each 28aa
> mer in each strand to simulate the strand being composed of 8 distinct
> units. When I do so, Amber just reconnects them. I assume this is because
> the consecutive C and N termini I wish to simulate are too close together.

This is not correct. Amber may not be recognizing your TER cards (you need
a space after the "TER" in earlier versions of the code. Of course, this is
just a guess, since you did not give any details of what you did. But Amber
would not ignore a TER card based on any distances in the structure.

....dac

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